United States Department of Agriculture

Marketing and Regulatory Programs

 Animal and Plant Health Inspection Service

 Veterinary Services

 VS Guidance 13403.1

1

Cleaning and Disinfecting Avian Quarantine Facilities Following Outbreaks of Newcastle 

Disease, Avian Influenza, or Other Communicable Avian Diseases

1. Purpose and Background

This guidance applies to the cleaning and disinfection of quarantine facilities used for 

commercial birds or poultry (including eggs for hatching of those commodities) after an 

outbreak of Newcastle disease (ND) or avian influenza (AI) of any subtype. It also 

establishes the timeline after which a quarantine facility that has undergone acceptable 

cleaning and disinfection may again be used for imported commercial birds or poultry (and 

eggs for hatching of those commodities).

(Note: At the facility operator’s discretion, facility employees may perform cleaning and 

disinfection following outbreaks of other communicable diseases of avians, although APHIS 

does not require this.)

This document represents the Agency’s current thinking on this topic. It does not create or 

confer any rights for or on any person and does not bind the U.S. Department of Agriculture 

(USDA) or the public. The information it contains may be made available to the public. While 

this document provides guidance for users outside Veterinary Services (VS), VS employees 

may not deviate from the directions provided herein without appropriate justification and 

supervisory concurrence.

2. Document Status

A. Review date: March 31, 2020.

B. This document replaces the Attachment associated with Veterinary Services 

Memorandum No 591.31, which is rescinded. The content of this document reflects and 

enhances the implementation of program changes. 

3. Reason for Reissuance

This is a new document.

4. Authority and References

A. Authorities (Code of Federal Regulations (CFR)):

• 7 CFR 371.4

• 9 CFR 71.10

• 9 CFR 93.100

• 9 CFR 93.106

• 9 CFR 93.209

• 9 CFR 93.210
 United States Department of Agriculture

Marketing and Regulatory Programs

 Animal and Plant Health Inspection Service

 Veterinary Services

 VS Guidance 13403.1

2

B. References

• VSG 13401.1, “APHIS Approval and Oversight of Privately Owned Avian Quarantine 

Facilities in the United States.”

• Procedures for Secure Transportation of AI-Infected Poultry Carcasses. 

• List of Environmental Protection Agency (EPA)-approved disinfectants for AI and ND.

• EPA-approved disinfectants for other types of pathogens. 

5. Audience 

VS employees, other Federal and State agencies, and members of the public.

6. Guidance

A. General (Non-Pathogen Specific) Cleaning and Disinfection Procedures

1) Use of personal protective equipment (PPE)

a. All personnel performing cleaning and disinfection in an avian quarantine facility 

should use PPE as identified in a site-specific job hazard analysis in accordance 

with Occupational Safety and Health Administration requirements.

b. All staff should be familiar with the Material Safety Data Sheets (MSDS and/or 

SDS) for disinfectants used on the premises.

2) Prior to disinfection, all carcasses, debris, manure, feathers, substrates and other

organic materials must be removed from the facility and disposed of via incineration 

or other approved method. (State regulations should be consulted for options for 

organic debris removal for other types of avian communicable outbreaks.) If 

incineration or other approved treatment is not performed onsite, a waste removal 

plan approved by the National Director for Animal Import Centers (NDAIC) or his or 

her designee, and that meets all relevant local, State, and Federal regulations, must 

be used. For additional information see Procedures for Secure Transportation of AIInfected Poultry Carcasses.

3) Most disinfectants, regardless of delivery method, work best at temperatures above 

65o F. The agent that causes avian influenza is heat labile; therefore, increasing 

temperatures of the disinfectant and/or the temperature in the facility increases the 

inactivation of the virus. When chlorine- and iodine-based disinfectants are used, the 

ambient temperature should not exceed 110o F. Adequate contact for disinfectants, 

as stated on the product label, is important for optimal performance. 
 United States Department of Agriculture

Marketing and Regulatory Programs

 Animal and Plant Health Inspection Service

 Veterinary Services

 VS Guidance 13403.1

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B. Cleaning and Disinfection Techniques for Pathogen Categories

1) For viral diseases such as AI and ND, APHIS or facility personnel should:

a. Clean all visible organic debris from all surfaces and equipment within quarantine 

areas, and wash thoroughly with hot water and a good quality detergent (any 

type containing surfactants).

b. If isolettes are used, change all types of air filtration.

c. Rinse all surfaces of detergents and allow complete drying before using 

disinfectants. APHIS personnel will approve adequacy of cleaning before 

disinfection takes place.

d. Disinfect all surfaces and equipment within quarantine areas using permitted 

disinfectants (listed at the end of this document). Follow the manufacturer’s label 

instructions, which include product concentration, temperature, and contact time. 

Although not specifically referenced in APHIS regulations, Virkon S and Maxima 

256 (both EPA-registered disinfectants) are 99 percent effective against AI and 

ND viruses, and are recommended by NVSL. Disinfectants listed in 9 CFR 71.10, 

or referenced on the EPA Web site for use against paramyxoviruses and 

orthomyxoviruses, may also be used (see the EPA web site or reference 9 CFR 

part 71 for more information). Allow all surfaces to dry completely.

e. Heating may alternatively be used for disinfection; ambient temperatures within 

any quarantined area must be maintained at 100° F for 6 days for AI virus and 

175° F for 6 days for ND virus.

f. After finishing any cleaning and disinfection after an AI or ND event, allow APHIS 

personnel to take samples from multiple locations within the areas of bird activity. 

Samples can be submitted to the NVSL as pooled (bundled into one plastic bag 

and shipped) or as individual samples with labels of specific locations collected. If 

submitting pooled samples that test positive, treat all sampled areas with 

comprehensive re-cleaning/disinfection until achieving a negative test result.

g. The NVSL may use polymerase chain reaction (PCR) test on samples submitted. 

If a performed PCR test has a positive result, the NVSL will use virus isolation as 

the definitive form of testing for AI and ND. APHIS personnel must specify the 

use of any other tests when submitting samples. The NVSL will report testing 

results to applicable APHIS personnel as set forth below. 
 United States Department of Agriculture

Marketing and Regulatory Programs

 Animal and Plant Health Inspection Service

 Veterinary Services

 VS Guidance 13403.1

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2) For bacterial and rickettsia diseases:

The importer of the shipment or State authorities, as applicable, will decide how to 

treat or dispose of birds affected by bacterial/rickettsia pathogens. The importer or 

State authorities must share any treatment/disposal plans with APHIS. APHIS has no 

specific regulations for infections caused by pathogens other than AI or ND; 

therefore, applicable APHIS personnel may consult internal Agency resources for

associated biosecurity concerns for other types of disease outbreaks. APHIS 

personnel may also follow the following guidance to achieve effective cleaning and 

disinfection:

a. Ensure all carcasses, debris, manure, feathers, and other organic material are 

removed from the facility and disposed of per a plan created with all applicable 

local, State, and Federal agencies. Pesticide application may be needed if 

infestation of insects, rodents, or other pests exists.

b. Clean organic debris from all surfaces and equipment within the quarantine areas 

and wash thoroughly with hot water and detergent containing surfactants.

c. Rinse all surfaces of detergents and allow complete drying before using 

disinfectants.

d. Disinfect all surfaces and equipment within quarantine areas using EPAregistered disinfectants for the pathogen of concern; follow all manufacturers’

label instructions. Concentration, temperature, and contact time are critical for 

product efficacy.

3) Fungal diseases: The importer or State officials, as appropriate, will decide how to 

treat or dispose of birds with fungal diseases. The importer or State official must 

share any treatment or disposal plans with APHIS. APHIS has no specific 

regulations for infections caused by pathogens other than AI or ND; applicable 

APHIS personnel may consult internal Agency resources for associated biosecurity 

concerns for other types of disease outbreaks. APHIS personnel may use the 

following guidance to achieve effective cleaning and disinfection:

a. Ensure all carcasses, debris, manure, feathers, and other organic material are 

removed from the facility and properly disposed in accordance with all applicable 

local, State, and Federal regulations.

b. Clean all visible organic debris from all surfaces and equipment within the 

quarantine areas and wash thoroughly with hot water and detergent containing 

surfactants.

c. Rinse all surfaces of detergents and allow complete drying before using 

disinfectants.
 United States Department of Agriculture

Marketing and Regulatory Programs

 Animal and Plant Health Inspection Service

 Veterinary Services

 VS Guidance 13403.1

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d. Disinfect all surfaces and equipment within quarantine areas using disinfectants 

registered by EPA for the pathogen of concern, while following all manufacturers’

label instructions, which includes product concentration, temperature, and 

contact time.

e. Allow all surfaces in the quarantine area to dry completely. Personnel may heat 

the quarantine area to 1000 F for 72 hours in addition to cleaning to disinfect it.

Note: Ambient temperature conditions, including temperature and relative humidity, 

will affect pathogen survival times.

C. Confirmatory Testing

1) Avian influenza and Newcastle disease outbreaks: After disinfection, APHIS 

personnel will conduct confirmatory testing of the facility’s disinfected hard surface 

areas. Personnel will submit samples to the NVSL for the appropriate assay (virus 

isolation, PCR, etc.). A quarantine facility must remain empty for 2 negative tests, 

separated by 7 days, with NVSL reporting results to APHIS personnel supervising 

the facility. Personnel must continue cleaning, disinfection, and/or heat cycles if any 

positive results occur, with testing cycles of 7 days in between sample submissions.

2) Other infectious disease outbreaks: Although APHIS has no specific regulations for 

cleaning of infectious diseases caused by pathogens other than AI or ND, the APHIS 

veterinary medical officer supervising the facility should use discretion for other types 

of disease outbreaks. State regulations may be followed for other avian 

communicable diseases. Personnel should not release avians from quarantine if 

other infectious disease is present and any animals show clinical signs of illness. 

Whether the facility is depopulated as a result of such outbreaks, the facility operator 

may pursue cleaning and disinfection for disease-affected areas of the quarantine 

facility per the recommendations in this guidance or through a facility-developed 

protocol.

3) The importer will be billed for VS services that may be part of or in addition to those 

in the cooperative service agreement.

D. Approved Disinfectants

1) Listed in 9 CFR 71.10:

a. Cresylic acid: 4 ounces in 1 gallon of water.

b. Liquefied phenol (87 percent strength): 6 fluid ounces in 1 gallon of water.

c. Chlorinated lime (30 percent available chlorine): 1 pound in 1 gallon of water.

2) Other disinfectants:
 United States Department of Agriculture

Marketing and Regulatory Programs

 Animal and Plant Health Inspection Service

 Veterinary Services

 VS Guidance 13403.1

6

a. Virkon S

b. Maxima 256

3) Brand names for common disinfectants

a. Sodium hypochlorite and other chlorine- based agents: bleach-Clorox®, 

Chloramine-T, Halazone®. Stock solution (works best in warm water): 1 ounce of

Clorox® in 1 gallon water. For a larger batch, use 1 cup Clorox® in 8 gallons of 

water.)

b. 4 Way Quaternary Ammonium: Roccal®, Germex®, Warden®

c. Phenols: Lysol®, Pine-sol®, 1-Stroke Environ®

Note: The EPA web site lists registered antimicrobial products with label claims for avian 

flu disinfectants. This site can be consulted for additional disinfectant 

resources/references. For use of cresylic acid as an official disinfectant, the National 

Director for Animal Import Centers (NDAIC), or his or her designee, must obtain, review, 

and approve specific manufacturer’s documentation of proposed use prior to granting 

approval.

7. Inquiries

Please direct any inquiries to:

Avian Import Specialist, Veterinary Services, National Import and Export Services (NIES)

301-851-3300, option 2; or VS-Live.Animals_Import.Permits@aphis.usda.gov.